Recognition of double helical DNA by purine oligonucleotides via triple helix formation

Oligonucleotide-directed triple helix formation is one of the most versatile methods for the sequence specific recognition of double helical DNA. Chapter 2 describes affinity cleaving experiments carried out to assess the recognition potential for purine-rich oligonucleotides via the formation of triple helices. Purine-rich oligodeoxyribonucleotides were shown to bind specifically to purine tracts of double helical DNA in the major groove antiparallel to the purine strand of the duplex. Specificity was derived from the formation of reverse Hoogsteen G•GC, A•AT and T•AT triplets and binding was limited to mostly purine tracts. This triple helical structure was stabilized by multivalent cations, destabilized by high concentrations of monovalent cations and was insensitive to pH. A single mismatched base triplet was shown to destabilize a 15 mer triple helix by 1.0 kcal/mole at 25°C. In addition, stability appeared to be correlated to the number of G•GC triplets formed in the triple helix. This structure provides an additional framework as a basis for the design of new sequence specific DNA binding molecules.

In work described in Chapter 3, the triplet specificities and required strand orientations of two classes of DNA triple helices were combined to target double helical sequences containing all four base pairs by alternate strand triple helix formation. This allowed for the use of oligonucleotides containing only natural 3'-5' phosphodiester linkages to simultaneously bind both strands of double helical DNA in the major groove. The stabilities and structures of these alternate strand triple helices depended on whether the binding site sequence was 5'-(purine)_m (pyrimidine)_n-3' or 5'- (pyrimidine)_m (purine)_n-3'.

In Chapter 4, the ability of oligonucleotide-cerium(III) chelates to direct the transesterfication of RNA was investigated. Procedures were developed for the modification of DNA and RNA oligonucleotides with a hexadentate Schiff-base macrocyclic cerium(III) complex. In addition, oligoribonucleotides modified by covalent attachment of the metal complex through two different linker structures were prepared. The ability of these structures to direct transesterification to specific RNA phosphodiesters was assessed by gel electrophoresis. No reproducible cleavage of the RNA strand consistent with transesterification could be detected in any of these experiments.

Preparation and characterization of an intramolecular electron transfer in a pentaammineruthenium derivative of Candida krisei cytochrome c

A semisynthetic binuclear metalloprotein has been prepared by appending the pentaammineruthenium moiety to histidine 39 of the cytochrome c from the yeast Candida krusei. The site of ruthenium binding was identified by peptide mapping. Spectroscopic and electrochemical properties of the derivative indicate the protein conformation is unperturbed by the modification. A preliminary (minimum) rate constant of 170s^(-1) has been determined for the intramolecular electron transfer from ruthenium(II) to iron(III), which occurs over a distance of at least 13Å (barring major conformational changes). Electrochemical studies indicate that this reaction should proceed with a driving force of ~170mV. The rate constant is an order of magnitude faster than that observed in horse heart cytochrome c for intramolecular electron transfer from pentaammineruthenium(II)(histidine 33) to iron(III) (over a similar distance, and with a similar driving force), suggesting a medium or orientation effect makes the Candida intramolecular electron transfer more favorable.

Measurement of two-photon excitation cross-section of a new symmetric-type fluorene derivative

A new dye, 2,7-bis(4-methoxystyryl)-9,9-bis(2-ethylhexyl)-9H-fluorene, has been synthesized, which is a D-pi-D symmetrical-type fluorene derivative. The two-photon absorption (TPA) of this new dye has been experimentally studied by comparable two-photon-induced fluorescence method. This new dye has a TPA cross-section of 84 x 10(-50) cm(4) s/photon at 790 nm/13 fs. (c) 2004 Elsevier GmbH. All rights reserved.

Weighted least-squares phase unwrapping algorithm based on derivative variance correlation map

Among different phase unwrapping approaches, the weighted least-squares minimization methods are gaining attention. In these algorithms, weighting coefficient is generated from a quality map. The intrinsic drawbacks of existing quality maps constrain the application of these algorithms. They often fail to handle wrapped phase data contains error sources, such as phase discontinuities, noise and undersampling. In order to deal with those intractable wrapped phase data, a new weighted least-squares phase unwrapping algorithm based on derivative variance correlation map is proposed. In the algorithm, derivative variance correlation map, a novel quality map, can truly reflect wrapped phase quality, ensuring a more reliable unwrapped result. The definition of the derivative variance correlation map and the principle of the proposed algorithm are present in detail. The performance of the new algorithm has been tested by use of a simulated spherical surface wrapped data and an experimental interferometric synthetic aperture radar (IFSAR) wrapped data. Computer simulation and experimental results have verified that the proposed algorithm can work effectively even when a wrapped phase map contains intractable error sources. (c) 2006 Elsevier GmbH. All rights reserved.

Three-photon absorption-induced fluorescence and optical limiting effects in a fluorene derivative

This paper reports on the steady-state fluorescence, three- photon absorption-induced fluorescence emission and subsequently induced optical limiting behaviour of a fluorene derivative with D-pi-D structural motifs. The lifetime of the steady-state fluorescence is 0.903 ns. Large optical limiting behaviour induced by 3PA has also been demonstrated, and the nonlinear absorption coefficient gamma derived from 3PA fitting curves is 5.92 x 10(-20) cm(3)/W-2 and the corresponding molecular 3PA cross-section sigma(3)' is 1.14 x 10(-76) cm(6) s(2).